Orders on Shopify that are fulfilled via FBA are handled via Amazon service known as Multi-Channel Fulfillment (MCF).
Sellers are responsible for providing customer service for their MCF orders. This includes handling requests for replacements, refunds, and returns. Amazon will not handle requests for returns and refunds.
Your customers will have to ship the products to you. Once you receive the products you can evaluate them and choose to refund the payment via Shopify admin.